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Phylogenetic analysis

Phylogenetic analysis. To infer and study evolutionary history  of homologous gene families. Manuel Ruiz (CIRAD, Data Integration team) Alexis Dereeper (IRD) Nathalie Chantret (INRA) Jean-François Dufayard (CIRAD, Data Integration team). Species evolutionary history.

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Phylogenetic analysis

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  1. Phylogenetic analysis To infer and study evolutionary history  of homologous gene families Manuel Ruiz (CIRAD, Data Integration team) Alexis Dereeper (IRD) Nathalie Chantret (INRA) Jean-François Dufayard (CIRAD, Data Integration team)

  2. Species evolutionary history Species phylogeny, and molecular phylogeny Species  phylogeny

  3. Species evolutionary history Species phylogeny, and molecular phylogeny Species phylogeny  Molecular evolutionary history Molecular phylogeny

  4. Species evolutionary history Species phylogeny, and molecular phylogeny Species phylogeny Modeling (trees) Molecular evolutionary history Molecular phylogeny Modeling (sequences, trees)

  5. Wheat Sequence 1 (wheat) Sequence 2 (rice) Rice Sequence 3 (tomato) Tomato Species phylogeny, and molecular phylogeny To infer evolutionary gene history... Permits to infer evolutionary species history ? What signal is supported by sequences ? Are speciations the only important events ?

  6. Wheat Rice Tomato Species phylogeny, and molecular phylogeny Duplication Sequence 1 (wheat) Sequence 2 (rice) Sequence 3 (tomato) Sequence 4  (wheat) Sequence 5 (rice) Sequence 6 (tomato)

  7. Wheat Rice Tomato Species phylogeny, and molecular phylogeny Gene losses Sequence 1 (wheat) Loss (rice) Sequence 3 (tomato) Loss  (wheat) Sequence 5 (rice) Loss (tomato)

  8. Wheat Rice Tomato Species phylogeny, and molecular phylogeny Losses Sequence 1 (wheat) Sequence 3 (tomato) Sequence 5 (rice)

  9. Wheat Rice Tomato Species phylogeny, and molecular phylogeny Tree reconciliation Sequence 1 (wheat) Sequence 1 (wheat) Loss (rice) Sequence 3 (tomato) Sequence 3 (tomato) Loss  (wheat) Sequence 5 (rice) Sequence 5 (rice) Loss (tomato)

  10. Sequence 1 (wheat) Sequence 2 (rice) Sequence 3 (tomato) Sequence 4  (wheat) Definitions Sequence 5 (rice) Sequence 6 (tomato) In silico Similarity: mathematical measure of similarity between two sequences (quantitative concept). Coverage: relative or absolute length along which two sequences are comparable. In vivo Homology: two molecules are homologous if they have derived from a common ancestral molecule (qualitative concept). Orthologous genes : genes derived from a common ancestor and diverged after a speciation event, they belong to different species. Paralogous genes : genes derived from a common ancestor and diverged after a duplication event, they can belong to the same species.

  11. 4 sequences from the reference transcriptome of Oryza sativa 1 mapped consensus sequence, for each individual (10 crop african rice et 1 wild african rice). Starting data Os2g25612 Os3g52163 Os4g66669 RC1 RC2 RC3 ... RS7

  12. Oryza sativa transcriptome: Sequence1_SATIVA Sequence2_SATIVA ... Consensus Oryza glaberima / Oryza barthii: Sequence1_RC1 Sequence2_RS1 ... Clustering: Retrieve homologous gene families Spot paralogies anterior to the Oryza sativa / Oryza glaberima divergence. Workflows Alignment and cleaning: Align similar portions between sequences, and select conserved bloc in order to support the homology hypothesis.  Phylogenetic reconstruction: Find a tree likely to explain the alignment in a given model of evolution. Interspecifique / inter-gender Intraspecifique / intra-gender Analyse: Display, rooting, reconciliation 

  13. Similar sequences from distant species: Sequence1_MAIZE Sequence2_SORBI ... Oryza sativa transcriptome: Sequence1_SATIVA Sequence2_SATIVA ... Consensus Oryza glaberima / Oryza barthii: Sequence1_RC1 Sequence2_RS1 ... Clustering: Retrieve homologous gene families Spot paralogies anterior to the Oryza sativa / Oryza glaberima divergence. BLAST on public databanks: Search homologous genes from several distant species Clarify the dates for duplication events Workflows Alignment and cleaning: Align similar portions between sequences, and select conserved bloc in order to support the homology hypothesis.  Phylogenetic reconstruction: Find a tree likely to explain the alignment in a given model of evolution. Interspecifique / inter-gender Intraspecifique / intra-gender Analyse: Display, rooting, reconciliation 

  14. BLAST : Homologous search in public databanks

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